{ "type": "genome", "identifier": "GCF_009176645.1", "organism": "Enterobacter oligotrophicus", "title": "Enterobacter oligotrophicus", "description": "na", "data type": "Genome sequencing and assembly", "organization": "Bioconversion Group, Research Institute for Sustainable Chemistry, Materials and Chemistry, National Institute of Advanced Industrial Science and Technology", "publication": [ {} ], "properties": { "assembly_accession": "GCF_009176645.1", "bioproject": "PRJNA224116", "biosample": "SAMD00143594", "wgs_master": "na", "refseq_category": "reference genome", "taxid": "2478464", "species_taxid": "2478464", "organism_name": "Enterobacter oligotrophicus", "infraspecific_name": "strain=CCA6", "isolate": "na", "version_status": "latest", "assembly_level": "Complete Genome", "release_type": "Major", "genome_rep": "Full", "seq_rel_date": "2019/03/18", "asm_name": "ASM917664v1", "asm_submitter": "Bioconversion Group, Research Institute for Sustainable Chemistry, Materials and Chemistry, National Institute of Advanced Industrial Science and Technology", "gbrs_paired_asm": "GCA_009176645.1", "paired_asm_comp": "identical", "ftp_path": "https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/176/645/GCF_009176645.1_ASM917664v1", "excluded_from_refseq": "na", "relation_to_type_material": "assembly from type material", "asm_not_live_date": "na ", "assembly_type": "haploid", "group": "bacteria", "genome_size": "4476585", "genome_size_ungapped": "4476585", "gc_percent": "54.500000", "replicon_count": "1", "scaffold_count": "1", "contig_count": "1", "annotation_provider": "NCBI RefSeq", "annotation_name": "GCF_009176645.1-RS_2024_03_28", "annotation_date": "2024-03-28", "total_gene_count": "4263", "protein_coding_gene_count": "4089", "non_coding_gene_count": "120", "pubmed_id": "31066221" }, "dbXrefs": [], "distribution": null, "Download": null, "status": "public", "visibility": null, "dateCreated": "2019-03-18", "dateModified": "2019-03-18", "datePublished": "2019-03-18", "_annotation": { "sample_count": 1, "sample_organism": [ "Enterobacter oligotrophicus" ], "sample_taxid": [ "2478464" ], "sample_host_organism": [], "sample_host_organism_id": [], "sample_host_disease": [], "sample_host_disease_id": [], "sample_host_location": [ "Japan:Hiroshima, Higashi-hiroshima" ], "sample_host_location_id": [], "data_size": "1.267 MB", "sample_ph_range": { "min": null, "max": null }, "sample_temperature_range": { "min": null, "max": null }, "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0, "genome_count": 1 }, "data_type": "G", "data_source": "RefSeq", "_dfast": { "Total Sequence Length (bp)": "4476585", "Number of Sequences": "1", "Longest Sequences (bp)": "4476585", "N50 (bp)": "4476585", "Gap Ratio (%)": "0.000000", "GCcontent (%)": "54.3", "Number of CDSs": "4134", "Average Protein Length": "321.0", "Coding Ratio (%)": "88.9", "Number of rRNAs": "25", "Number of tRNAs": "88", "Number of CRISPRs": "2" }, "has_analysis": true, "_dfastqc": { "tc_result": [ { "organism_name": "Enterobacter oligotrophicus", "strain": "strain=CCA6", "accession": "GCA_009176645.1", "taxid": 2478464, "species_taxid": 2478464, "relation_to_type": "type", "validated": true, "ani": 100.0, "matched_fragments": 1488, "total_fragments": 1492, "ani_threshold": 95, "status": "conclusive" }, { "organism_name": "Enterobacter quasimori", "strain": "strain=090044", "accession": "GCA_003964905.1", "taxid": 2838947, "species_taxid": 2838947, "relation_to_type": "type", "validated": true, "ani": 88.7003, "matched_fragments": 1241, "total_fragments": 1492, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter mori", "strain": "strain=LMG 25706", "accession": "GCA_000211415.1", "taxid": 539813, "species_taxid": 539813, "relation_to_type": "type", "validated": true, "ani": 88.6193, "matched_fragments": 1167, "total_fragments": 1492, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter asburiae", "strain": "strain=ATCC 35953", "accession": "GCA_001521715.1", "taxid": 61645, "species_taxid": 61645, "relation_to_type": "type", "validated": true, "ani": 88.3744, "matched_fragments": 1169, "total_fragments": 1492, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter asburiae", "strain": "strain=FDAARGOS_892", "accession": "GCA_016027695.1", "taxid": 61645, "species_taxid": 61645, "relation_to_type": "type", "validated": true, "ani": 88.368, "matched_fragments": 1167, "total_fragments": 1492, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter wuhouensis", "strain": "strain=WCHEW120002", "accession": "GCA_004331265.1", "taxid": 2529381, "species_taxid": 2529381, "relation_to_type": "type", "validated": true, "ani": 88.3262, "matched_fragments": 1276, "total_fragments": 1492, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter hormaechei subsp. oharae", "strain": "strain=FDAARGOS_1533", "accession": "GCA_020097195.1", "taxid": 301102, "species_taxid": 158836, "relation_to_type": "type", "validated": true, "ani": 88.3248, "matched_fragments": 1232, "total_fragments": 1492, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter hormaechei subsp. oharae", "strain": "strain=DSM 16687", "accession": "GCA_001729705.1", "taxid": 301102, "species_taxid": 158836, "relation_to_type": "type", "validated": true, "ani": 88.3189, "matched_fragments": 1233, "total_fragments": 1492, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter bugandensis", "strain": "", "accession": "GCA_900324475.1", "taxid": 881260, "species_taxid": 881260, "relation_to_type": "type", "validated": true, "ani": 88.3069, "matched_fragments": 1240, "total_fragments": 1492, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter bugandensis", "strain": "strain=FDAARGOS 1427", "accession": "GCA_019046905.1", "taxid": 881260, "species_taxid": 881260, "relation_to_type": "type", "validated": true, "ani": 88.3025, "matched_fragments": 1226, "total_fragments": 1492, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter roggenkampii", "strain": "strain=DSM 16690", "accession": "GCA_024390995.1", "taxid": 1812935, "species_taxid": 1812935, "relation_to_type": "type", "validated": true, "ani": 88.2154, "matched_fragments": 1158, "total_fragments": 1492, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter hormaechei subsp. steigerwaltii", "strain": "strain=DSM 16691", "accession": "GCA_001729725.1", "taxid": 299766, "species_taxid": 158836, "relation_to_type": "type", "validated": true, "ani": 88.2079, "matched_fragments": 1252, "total_fragments": 1492, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter hormaechei", "strain": "strain=FDAARGOS 1433", "accession": "GCA_019048245.1", "taxid": 158836, "species_taxid": 158836, "relation_to_type": "suspected-type", "validated": true, "ani": 88.1977, "matched_fragments": 1225, "total_fragments": 1492, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter hormaechei subsp. hormaechei", "strain": "strain=ATCC 49162", "accession": "GCA_001875655.1", "taxid": 301105, "species_taxid": 158836, "relation_to_type": "type", "validated": true, "ani": 88.1631, "matched_fragments": 1236, "total_fragments": 1492, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter hormaechei subsp. hormaechei", "strain": "strain=ATCC 49162", "accession": "GCA_000213995.1", "taxid": 301105, "species_taxid": 158836, "relation_to_type": "type", "validated": true, "ani": 88.0235, "matched_fragments": 1219, "total_fragments": 1492, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter cloacae", "strain": "strain=DSM 30054", "accession": "GCA_021469225.1", "taxid": 550, "species_taxid": 550, "relation_to_type": "type", "validated": true, "ani": 87.8093, "matched_fragments": 1223, "total_fragments": 1492, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter sichuanensis", "strain": "strain=WCHECL1597", "accession": "GCA_025002605.1", "taxid": 2071710, "species_taxid": 2071710, "relation_to_type": "type", "validated": true, "ani": 87.7936, "matched_fragments": 1185, "total_fragments": 1492, "ani_threshold": 95, "status": "below_threshold" }, { "organism_name": "Enterobacter cancerogenus", "strain": "", "accession": "GCA_900185905.1", "taxid": 69218, "species_taxid": 69218, "relation_to_type": "type", "validated": true, "ani": 87.3912, "matched_fragments": 1259, "total_fragments": 1492, "ani_threshold": 95, "status": "below_threshold" } ], "cc_result": { "completeness": 100.0, "contamination": 0.0, "strain_heterogeneity": 0.0 }, "gtdb_result": [ { "accession": "GCF_009176645.1", "gtdb_species": "s__Enterobacter oligotrophicus", "ani": 100.0, "matched_fragments": 1490, "total_fragments": 1492, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.55", "min_intra_species_ani": "99.09", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.94", "num_clustered_genomes": 3, "status": "conclusive" }, { "accession": "GCF_000211415.1", "gtdb_species": "s__Enterobacter mori", "ani": 88.6145, "matched_fragments": 1168, "total_fragments": 1492, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "97.59", "min_intra_species_ani": "96.13", "mean_intra_species_af": "0.88", "min_intra_species_af": "0.85", "num_clustered_genomes": 23, "status": "-" }, { "accession": "GCF_003634515.1", "gtdb_species": "s__Enterobacter asburiae_A", "ani": 88.3764, "matched_fragments": 1201, "total_fragments": 1492, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 96.0274, "mean_intra_species_ani": "97.62", "min_intra_species_ani": "96.46", "mean_intra_species_af": "0.91", "min_intra_species_af": "0.85", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_001521715.1", "gtdb_species": "s__Enterobacter asburiae", "ani": 88.3744, "matched_fragments": 1169, "total_fragments": 1492, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 96.8818, "mean_intra_species_ani": "98.42", "min_intra_species_ani": "96.92", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.84", "num_clustered_genomes": 32, "status": "-" }, { "accession": "GCF_007035645.1", "gtdb_species": "s__Enterobacter asburiae_B", "ani": 88.341, "matched_fragments": 1187, "total_fragments": 1492, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 96.8818, "mean_intra_species_ani": "98.31", "min_intra_species_ani": "97.34", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.85", "num_clustered_genomes": 70, "status": "-" }, { "accession": "GCF_009755685.1", "gtdb_species": "s__Enterobacter sp000568095", "ani": 88.3069, "matched_fragments": 1215, "total_fragments": 1492, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 95.0476, "mean_intra_species_ani": "98.37", "min_intra_species_ani": "98.04", "mean_intra_species_af": "0.95", "min_intra_species_af": "0.92", "num_clustered_genomes": 11, "status": "-" }, { "accession": "GCF_900324475.1", "gtdb_species": "s__Enterobacter bugandensis", "ani": 88.3047, "matched_fragments": 1240, "total_fragments": 1492, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.49", "min_intra_species_ani": "95.52", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.88", "num_clustered_genomes": 115, "status": "-" }, { "accession": "GCF_011754535.1", "gtdb_species": "s__Enterobacter cloacae_N", "ani": 88.2786, "matched_fragments": 1217, "total_fragments": 1492, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.03", "min_intra_species_ani": "98.99", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.91", "num_clustered_genomes": 4, "status": "-" }, { "accession": "GCF_003594915.1", "gtdb_species": "s__Enterobacter chuandaensis", "ani": 88.2439, "matched_fragments": 1208, "total_fragments": 1492, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.38", "min_intra_species_ani": "98.32", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.92", "num_clustered_genomes": 3, "status": "-" }, { "accession": "GCF_008364625.1", "gtdb_species": "s__Enterobacter dykesii", "ani": 88.2093, "matched_fragments": 1145, "total_fragments": 1492, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 96.5795, "mean_intra_species_ani": "99.13", "min_intra_species_ani": "97.97", "mean_intra_species_af": "0.97", "min_intra_species_af": "0.95", "num_clustered_genomes": 7, "status": "-" }, { "accession": "GCF_001729745.1", "gtdb_species": "s__Enterobacter hormaechei_A", "ani": 88.1673, "matched_fragments": 1244, "total_fragments": 1492, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "96.63", "min_intra_species_ani": "95.22", "mean_intra_species_af": "0.89", "min_intra_species_af": "0.83", "num_clustered_genomes": 1867, "status": "-" }, { "accession": "GCF_008080435.1", "gtdb_species": "s__Enterobacter asburiae_C", "ani": 88.1587, "matched_fragments": 1201, "total_fragments": 1492, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 95.5575, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" }, { "accession": "GCF_001875655.1", "gtdb_species": "s__Enterobacter hormaechei", "ani": 88.1551, "matched_fragments": 1235, "total_fragments": 1492, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.46", "min_intra_species_ani": "98.52", "mean_intra_species_af": "0.92", "min_intra_species_af": "0.86", "num_clustered_genomes": 32, "status": "-" }, { "accession": "GCF_900322725.1", "gtdb_species": "s__Enterobacter quasihormaechei", "ani": 88.0089, "matched_fragments": 1223, "total_fragments": 1492, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "99.46", "min_intra_species_ani": "97.61", "mean_intra_species_af": "0.96", "min_intra_species_af": "0.89", "num_clustered_genomes": 41, "status": "-" }, { "accession": "GCF_008364555.1", "gtdb_species": "s__Enterobacter vonholyi", "ani": 87.9907, "matched_fragments": 1148, "total_fragments": 1492, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.34", "min_intra_species_ani": "98.09", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.93", "num_clustered_genomes": 8, "status": "-" }, { "accession": "GCF_013375935.1", "gtdb_species": "s__Enterobacter cloacae_O", "ani": 87.8064, "matched_fragments": 1235, "total_fragments": 1492, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.68", "min_intra_species_ani": "98.59", "mean_intra_species_af": "0.94", "min_intra_species_af": "0.92", "num_clustered_genomes": 6, "status": "-" }, { "accession": "GCF_019047785.1", "gtdb_species": "s__Enterobacter cancerogenus", "ani": 87.5434, "matched_fragments": 1245, "total_fragments": 1492, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "98.78", "min_intra_species_ani": "98.42", "mean_intra_species_af": "0.93", "min_intra_species_af": "0.90", "num_clustered_genomes": 16, "status": "-" }, { "accession": "GCF_003057745.1", "gtdb_species": "s__Enterobacter sp003057745", "ani": 86.8947, "matched_fragments": 1165, "total_fragments": 1492, "gtdb_taxonomy": "d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Enterobacter", "ani_circumscription_radius": 95.0, "mean_intra_species_ani": "N/A", "min_intra_species_ani": "N/A", "mean_intra_species_af": "N/A", "min_intra_species_af": "N/A", "num_clustered_genomes": 1, "status": "-" } ] }, "_bac2feature": { "phenotypes": null, "cell_diameter": null, "cell_length": null, "doubling_h": null, "growth_tmp": 31.181, "optimum_tmp": 31.5, "optimum_ph": 5.75, "genome_size": 4862814.485, "gc_content": 55.35, "coding_genes": 4535.096, "rRNA16S_genes": 7.95, "tRNA_genes": 84.309, "gram_stain": 0.0, "sporulation": 0.0, "motility": 0.833, "range_salinity": 1.0, "facultative_respiration": 0.428, "anaerobic_respiration": 0.0, "aerobic_respiration": 0.571, "mesophilic_range_tmp": 1.0, "thermophilic_range_tmp": 0.0, "psychrophilic_range_tmp": 0.0, "bacillus_cell_shape": 1.0, "coccus_cell_shape": 0.0, "filament_cell_shape": 0.0, "coccobacillus_cell_shape": 0.0, "vibrio_cell_shape": 0.0, "spiral_cell_shape": 0.0 }, "_genome_taxon": [ "Enterobacter", "oligotrophicus" ], "quality": 5, "quality_label": "\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f\u2b50\ufe0f" }